Results for “alphafold”

3 skills

alterlab-alphafold-db

Access the AlphaFold DB of 200M+ AI-PREDICTED protein structures — retrieve models by UniProt accession, download PDB/mmCIF files, and analyze prediction confidence metrics (pLDDT, PAE). Use when a UniProt ID needs a computationally predicted 3D structure or when no experimental structure exists, for homology modeling, protein engineering, or structure-based drug discovery; for EXPERIMENTALLY determined structures (X-ray, cryo-EM, NMR) prefer alterlab-pdb, and for protein sequences, annotations, or accession ID mapping prefer alterlab-uniprot instead. Part of the AlterLab Academic Skills suite.

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alterlab-datamol

Wraps RDKit in a high-level, pandas-friendly datamol interface with sensible defaults for everyday drug discovery — SMILES/SDF loading into DataFrames, molecule standardization, descriptors, fingerprints, Butina clustering, 3D conformer generation, scaffold analysis, and parallel batch processing, returning native rdkit.Chem.Mol objects. Use when running standard cheminformatics pipelines on molecule tables with minimal boilerplate; for low-level control, custom sanitization, or specialized algorithms prefer alterlab-rdkit. Part of the AlterLab Academic Skills suite.

Access the RCSB Protein Data Bank (PDB) for EXPERIMENTALLY determined 3D structures (X-ray, cryo-EM, NMR) of proteins and nucleic acids — searching by text, sequence, or structure similarity and downloading coordinates in PDB/mmCIF format with metadata. Use when retrieving a structure by PDB ID, running sequence or structure similarity searches, or obtaining experimental coordinates for structural biology and drug discovery; for AI-PREDICTED structures of proteins lacking experimental data prefer alterlab-alphafold-db, and for protein sequences, annotations, or accession ID mapping prefer alterlab-uniprot instead. Part of the AlterLab Academic Skills suite.